Protein Stability and Protein Folding

Protein stability is the net balance of forces which allow someone to tell whether or not the protein will be denatured. This is also referred to as thermodynamic stability. The net stability can be defined as the difference in free energy between the native and denatured state. These two values can be called Gn and Gu.

In the previous blog post, free energy was introduced as related to free energy. The Gibbs Free Energy value can be calculated using a variety of equations. In fact, there are four ways to calculate this value. The four ways include delta G = delta H - T (delta S), the difference between the free energies of products and reactants, Hess's Law, and delta G = delta Go + RTlnQ.

Decreasing the energy of the folded state or increasing the energy of the unfolded state have the same effect on delta G. The equation normally used to calculate the free energy can be taken from delta G = Gn - Gu = -RTlnK. In this case, the K would be equal to the fraction folded divided by the fraction unfolded. The reason why this practice has so much significance is because of the multitude of drugs that can be made if different proteins were seen as more stable. Various new formulas for different protein combinations can be made, which may be able to make them safer to sell in pharmacies.

We will take this formula and put it into good use through practice! We can measure the difference in free energy in the unfolded and folded states. The average stability of a monomeric small protein is about 5-10 kcal/mol. Therefore, when plugged into the equation, an aqueous solution at room temperature would have a ratio of 20000000:1 in terms of folded to unfolded. This value of K can also be looked at as the ratio of the forward and reverse rate constants. When delta G is graphed against Denaturant or Urea, the graph typically comes out to be downward sloping, signalling a drop in the amount of free energy changed.

The Van't Hoff Equation can also be written as dlnK/d(1/T) = -H/R. Thus, when Van'T Hoff plots (lnK vs. 1/T) are made, the thermal denaturation of proteins are non-linear, indicating that H varies with temperature. This implies that the heat capacity for the folded and unfolded proteins are different.

Free Energy of Protein Folding

There are a lot of benefits of understanding the free energy in protein folding. First, many proteins are used in industrialized products, including in a lot of what one puts into the body. These proteins must be stable in order to be taken in by the body. If these proteins have a slight risk of being bad for people, then these proteins cannot be sold to consumers. Another reason protein sequencing would be beneficial is because researchers believe that proteins can be denatured and still work. Instead of maintaining their shape, the proteins can still do daily life functions. One last reason why protein sequencing is helpful is because it can limit the amount of procedures that need to be done to the proteins. Some of the superfluous procedures, including X-rays crystallography and Nuclear Magnetic Resonance, will not need to be performed anymore if scientists had a better understanding of free energy.

Before we understand free energy in protein folding, we must understand free energy. Gibbs free energy, synonymous with free energy, is defined as the enthalpy of the system minus the product of the temperature times the entropy of the system. This is denoted by the equation G = H - TS. The free energy of the system is a state function because the thermodynamic functions inside of the equation, including H and S, are both state functions as well. If you want to know more, watch the video provided. It is a presentation by Paul Andersen explaining Gibbs free energy.

When proteins denature, then the primary functions of the proteins do not work. The willingness and ability for proteins to be flexible is calculated by measuring the free energy of various proteins. However, this free energy value might be more and more difficult to solve because there is a different energy landscape for each state of the protein, whether it is neutral, charged, folded, intermediate, or even unfolded. These various states allow there to be many mistakes that can occur when trying to calculate the free energy of a system. Therefore, if we understand the protein sequences better, the free energy might be easier to solve for. The state in which it is in might be able to help scientists predict what the value of the free energy is. Next post we will look into how to actually calculate this value and what state the protein must be in.